It is only on the popular trails that you have to plug your nose. Although I'm not happy about the conditions you ran into, I am happy that the bulk of the traffic stays in certain popular areas in the Sierra because that leaves the bulk of the backcountry fairly pristine.
I wish this were true. When I am on the JMT or other high traffic trails, I am not terribly surprised when I see signs of human impact---trash, unburied human waste, soap bubbles in the water, somebody's uneaten Ramen noodles at the lake edge, etc. What I find most heartbreaking though is when I find these same signs of human impact far off-trail. One of my favorite things about traveling cross country is the sense that you are seeing a place that very few others have visited. I also love not having to purify my drinking water.
Last July, while hiking the section of the SHR between N. Glacier Pass and Tuolumne, I was reveling in the apparent "pristine" quality of Bench Canyon. No sooner were the words out of my mouth, I was horrified to encounter a giant pile of unburied human poo in a sandy patch perhaps 50 feet from where we had pitched our tent complete with a equally giant wad of T.P. Granted, one has to work pretty hard to get to Bench Canyon----there is no easy way in or out. It absolutely killed me that someone who had the backpacking chops to get to a place such as Bench Canyon could be so lazy, ignorant and self-absorbed. Over the years, I've sadly found lots of soap bubbles eddied out in backcountry streams and lakes. I think, perhaps, some people take the "biodegradable" label on their Camp Suds a bit too literally and wash themselves and their pots directly in the stream. So, I totally get the rant of the original poster. I share your pain.